Train Prague to Krakow

RyanAir has nonstop flights scheduled from Prague to Krakow on Mondays and Fridays in May, 2020.

Train schedules will probably be similar to what they are now, with one direct daytime train departing Prague about 10:25 to arrive at 17:30 and one direct overnight train. I've taken that night train with no problem. You can book tickets at www.cd.cz starting about 60 days in advance, as well as in stations.

We recently got notification from American Airlines that our Flight to
Krakow got cancelled(route change) and gave us option to fly into
Prague.

Have you tried to get a different flight to Krakow? It's odd that an airline's "Plan B" has you flying into a whole different country. You can/should request something comparable to your original flight. I've had an awful time with American Airlines due to these kinds of changes (which seemed excessive) so I just cancelled the flight (my last straw with them) and booked a better itinerary for less with another airline. You still have plenty of time, so that's always an option.

We looked after flight was cancelled/changed there were no other good flight PHL to KRK, only 2 connections poor flights and 24 hours to get there, We are now on a non-stop flight PHL-PRG. I looked at this as an opportunity to visit another country on our list. We booked with points RT airfare was only $32 each including seats and a free bag. It limited our choices.
Now we just have to figure best way to get to Poland. I can get LOT airline flight to WAW, but no direct flights to KRK on Saturday or Sundays

I took the train from Prague to Krakow a few years ago (2014) and it was fine. It's a long train ride but it would be just as long to fly to Warsaw and then train to Krakow. Train was comfortable and relaxing. I can't help with advance tickets because I purchased mine at the Prague train station a couple of days before travel and paid the full price - poor planning on my part. Check Seat 61 for info on tickets in advance.

I checked Ceske Drahy site, cd.cz/en Tickets are not for sale past Dec 14, the date of European wide schedule updates. But for Saturday, Dec 14, the 10:24 direct train to Krakow has second class tickets for 446 CZK per person. That's about $22 US. If you want 1st class, its 887 CZK, about $39 US. Those are nonrefundable tickets bought now.

Thanks for info

The website "the man in Seat 61" has great information on travel among destinations in Europe.

https://www.seat61.com

https://www.seat61.com/trains-and-routes/prague-to-krakow-by-train.htm

But check updates closer to your trip.